Six novel murine homeobox genes, Uncx-4.1, OG-2, OG-9, Prx3/OG-12, OG- 22, and NKx-1.2 were cloned and partially sequenced. Two species of Prx3 cDNAs that correspond to alternatively spliced species of Prx3 mRNA were cloned from mouse cDNA libraries. Prx3 RNA was found in the brain and in non neuronale structures around the oral cavity, hip and shoulder of mouse embryos. More than ten kb of NKx-1.2 genomic DNA, and several NKx-1.2 cDNAs were sequenced. NKx poly-A+ RNA from adult mouse brain and mouse embryos contains major species of NKx-1.2 RNA, whereas RNA from testes contains at least three bands of NKx-1.2 mRNA. NKx-1.2 mRNA was found in the mesencephalon, myelencephalon, spinal cord, vertebrae, and ribs of 12 day mouse embryos, and in distinct patches in the pons and diencephalon of 14 day mouse embryos. Several species of NKx-1.2 cDNA were cloned from mouse testis mRNA. Chimeric mice that bear a NKx-1.2 transgene were obtained by homologous recombination. Two species of OG-22/mCart-1 cDNA were found in mouse embryo cDNA libraries that correspond to alternatively spliced species of OG- 22/mCart-1 mRNA. OG-22/mCart-1 mRNA is expressed in the head and brachial arches of mouse embryos, and in adult mouse lung and testis.Four species of Uncx-4.1 cDNA encoding different forms of Uncx-4.1 protein were cloned from mouse embryo mRNA and brain, and testis of adult mice. Two species of OG-9 mRNA were detected in adult skeletal muscle and brain. Several species of OG-9 mRNA were cloned from mouse brain mRNA. Two species of OG-9 mRNA were found in embryos; the highest levels of OG-9 mRNA were detected in late embryos. Southern analysis suggests that the OG-9 gene and another closely related are present in the mouse genome. One major transcript of OG-2 mRNA is found in 15-17 day mouse embryos; a shorter species of OG-2 mRNA was found in younger embryos. OG-2 cDNA clones were obtained from mouse embryos that correspond to three alternatively spliced forms of OG-2 mRNA. OG- 2 mRNA also was found in adult mouse skeletal muscle, brain, testes, and heart.